Data from: Evaluating summary methods for multi-locus species tree estimation in the presence of incomplete lineage sorting

Species tree estimation is complicated by processes, such as gene duplication and loss and incomplete lineage sorting (ILS), that cause discordance between gene trees and the species tree. Furthermore, while concatenation, a traditional approach to tree estimation, has excellent performance under many conditions, the expectation is that the best accuracy will be obtained through the use of species tree estimation methods that are specifically designed to address gene tree discordance. In this paper, we report on a study to evaluate MP-EST – one of the most popular species tree estimation methods designed to address ILS – as well as concatenation under maximum likelihood, the greedy consensus, and two supertree methods (MRP and MRL). Our study shows that several factors impact the absolute and relative accuracy of methods, including the number of gene trees, the accuracy of the estimated gene trees, and the amount of ILS. Concatenation can be more accurate than the best summary methods in some cases (mostly when the gene trees have poor phylogenetic signal or when the level of ILS is low), but summary methods are generally more accurate than concatenation when there are an adequate number of sufficiently accurate gene trees. Our study suggests that coalescent-based species tree methods may be key to estimating highly accurate species trees from multiple loci.物种树推断（species tree estimation）的复杂度常受基因重复与丢失、不完全谱系分选（incomplete lineage sorting, ILS）等过程影响，这类过程会导致基因树（gene tree）与物种树（species tree）间出现拓扑冲突。此外，尽管传统的物种树推断方法串联法（concatenation）在诸多条件下具备出色性能，但学界普遍认为，唯有采用专门针对基因树冲突问题设计的物种树推断方法，方可获得最优的推断精度。本文报道了一项评估研究的结果：该研究对MP-EST——专为解决ILS问题设计的主流物种树推断方法之一——、基于最大似然法（maximum likelihood）的串联分析、贪婪一致树法（greedy consensus），以及两种超树方法（supertree methods）MRP与MRL的性能进行了评估。研究结果显示，多项因素会影响各方法的绝对与相对精度，包括基因树的数量、估算所得基因树的精度，以及ILS的发生水平。在部分场景下（多为基因树系统发育信号较弱或ILS水平较低时），串联法的精度可优于最优的摘要类方法；但当拥有足够数量且精度达标的基因树时，摘要类方法的整体精度通常高于串联法。本研究表明，基于溯祖理论的物种树推断方法，或可成为从多个基因座（multiple loci）推断高精度物种树的关键手段。